Microbial communities in the food chain: application of whole genome sequencing and metagenomics to investigate interactions between pathogens, commen

食源性疾病仍然是一个国家和全球健康问题。根据食品标准局（2011年），估计每年约有100万人患有食源性疾病，其中约20，000人需要住院治疗，500人死于食源性疾病。英国与食源性疾病相关的费用估计为15亿英镑。考虑到食源性疾病的公共卫生影响和经济影响，重要的是要更好地了解食源性病原体在食品生产链中的分布，并开发可靠和快速的食源性病原体检测和跟踪方法，特别是导致大量食源性疾病病例的病原菌。众所周知，周围环境会对细菌种群造成压力，并导致微生物群落的重组，这些都有可能影响食品生产链中致病菌的持久性。包括2018年法国与婴儿配方奶粉有关的沙门氏菌病爆发在内的一些疫情表明了理解持久性和影响因素的重要性，以便制定预防这种情况发生的策略。组学技术的出现使微生物群落的表征及其对病原体存在的影响方面的进展成为可能。例如，宏基因组学最近已被用于食品和食物链环境中病原体的检测、鉴定和表征。它提供了一个机会，看看多样性和动态丰富的病原体在一个样本中以公正的方式，并被用来改善基于培养的富集方法。鸟枪宏基因组学可以提供一个有价值的，快速查看的存在遗传标记指定物种，血清型，毒力和抗菌素耐药基因等，虽然，目前，这些标记不能分配到特定的细菌基因组由于宏基因组数据的复杂性。未来的宏基因组学和元条形码生物信息学的发展可能会使这一点和研究致病性的能力成为可能，并可能允许在病原体（如沙门氏菌）和更广泛的亚群（如肠杆菌科）之间建立联系。培养法和全基因组测序法可以作为病原体确认和追踪的补充方法。亿滋希望探索这些新技术的应用，以更好地了解食品制造环境中病原体的持久性，从而开发预防方法，并确定去除持久性有害微生物的策略。为此，亿滋国际对病原体持久性的基本理解以及更广泛的细菌群落之间的相互作用感兴趣，以确定技术方法来确定病原体存在的标志物并通过食物链追踪病原体。确定和描述从指定食品生产环境中回收的沙门氏菌之间的遗传关系;并阐明基于非培养方法的动态定殖模式，以发现新的自然作用生物控制策略

Foodborne illness remains a national and global health concern. According to the Food Standards Agency (2011), it is estimated that around 1 million people suffer a foodborne illness every year, with approximately 20,000 requiring hospital treatment and 500 deaths resulting from foodborne illness. The costs associated with foodborne disease in the UK are estimated to be £1.5 billion. Considering the public health impact and economic impact of foodborne illness, it is important to better understand the distribution of foodborne pathogens in food production chains and to develop reliable and rapid methods for foodborne pathogen detection and tracking, particularly pathogenic bacteria that cause a large-numbers of cases of foodborne disease. It is well known that surrounding environments cause stresses on bacterial populations and lead to reorganisation of microbial communities and these have the potential to influence the persistence of pathogenic bacteria in the food production chain. A number of outbreaks including the recent salmonellosis outbreak in France linked to infant formula in 2018 serve to demonstrate the importance of understanding persistence and the factors that influence this, in order to develop strategies to prevent this occurring. The advent of omics technologies enables advances in relation to characterization of microbial communities and their influence on the presence of pathogens. For example, metagenomics has recently been used for the detection, identification and characterisation of pathogens in food and in the food chain environment. It provides an opportunity to look at the diversity and the dynamic abundance of pathogens within a sample in an unbiased manner and is being used to improve culture-based enrichment methods. Shotgun metagenomics can provide a valuable, rapid view of the presence of genetic markers specifying species, serotype, virulence and antimicrobial resistance genes etc. although, at present, these markers cannot be assigned to specific bacterial genomes due to the complexity of the metagenomic data. Future metagenomic and metabarcoding bioinformatic developments are likely to make this and the ability to investigate phylogeny possible, and perhaps allow links to be drawn between presence of pathogens, such as Salmonella, and wider sub-groups, such as the Enterobacteriaceae. Culture-based methods followed by whole-genome sequencing may be used as a complementary approach to allow pathogen confirmation and tracking.Mondelez would like to explore application of these new techniques to better understand persistence of pathogens in food manufacturing settings with the aim of developing approaches to prevent occurrence and to identify strategies to remove persisting unwanted microorganisms. To that effect, Mondelez is interested in the fundamental understanding of pathogen persistence and the interactions between the wider bacterial communities to identify technological approaches to identify markers for pathogen presence and for tracking pathogens through the food chain. To characterise and describe the genetic relationships between a collection of Salmonella species recovered from a designated food production environment; and elucidate the dynamic colonisation patterns based on culture-independent methods to discover novel naturally-acting biocontrol strategies